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A roadmap of constitutive NF-κB activity in Hodgkin lymphoma: Dominant roles of p50 and p52 revealed by genome-wide analyses.

de Oliveira KA, Kaergel E, Heinig M, Fontaine JF, Patone G, Muro EM, Mathas S, Hummel M, Andrade-Navarro MA, Hübner N, Scheidereit C.

Genome Med. 2016 Mar 17;8(1):28. doi: 10.1186/s13073-016-0280-5.


Work-related respiratory symptoms in Champagne vineyard workers.

Perotin JM, Barbe C, Nguyen KL, Fontaine JF, Gabignon Y, Nardi J, Launois C, Lebargy F, Lavaud F, Deslee G.

Eur Ann Allergy Clin Immunol. 2015 Sep;47(5):140-4.


Comparison of the strain field of abdominal aortic aneurysm measured by magnetic resonance imaging and stereovision: a feasibility study for prediction of the risk of rupture of aortic abdominal aneurysm.

Wang Y, Joannic D, Delassus P, Lalande A, Juillion P, Fontaine JF.

J Biomech. 2015 Apr 13;48(6):1158-64. doi: 10.1016/j.jbiomech.2015.01.017. Epub 2015 Jan 21.


Assessment of curated phenotype mining in neuropsychiatric disorder literature.

Fontaine JF, Priller J, Spruth E, Perez-Iratxeta C, Andrade-Navarro MA.

Methods. 2015 Mar;74:90-6. doi: 10.1016/j.ymeth.2014.11.022. Epub 2014 Dec 5.


A lymph node ratio of 10% is predictive of survival in stage III colon cancer: a French regional study.

Sabbagh C, Mauvais F, Cosse C, Rebibo L, Joly JP, Dromer D, Aubert C, Carton S, Dron B, Dadamessi I, Maes B, Perrier G, Manaouil D, Fontaine JF, Gozy M, Panis X, Foncelle PH, de Fresnoy H, Leroux F, Vaneslander P, Ghighi C, Regimbeau JM; APCD-LNR-2011 study group.

Int Surg. 2014 Jul-Aug;99(4):344-53. doi: 10.9738/INTSURG-D-13-00052.1.


Alkemio: association of chemicals with biomedical topics by text and data mining.

Gijón-Correas JA, Andrade-Navarro MA, Fontaine JF.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W422-9. doi: 10.1093/nar/gku432. Epub 2014 May 16.


[Birch pollen allergy].

Lavaud F, Fore M, Fontaine JF, Pérotin JM, de Blay F.

Rev Mal Respir. 2014 Feb;31(2):150-61. doi: 10.1016/j.rmr.2013.08.006. Epub 2013 Nov 9. Review. French.


CellFinder: a cell data repository.

Stachelscheid H, Seltmann S, Lekschas F, Fontaine JF, Mah N, Neves M, Andrade-Navarro MA, Leser U, Kurtz A.

Nucleic Acids Res. 2014 Jan;42(Database issue):D950-8. doi: 10.1093/nar/gkt1264. Epub 2013 Dec 3.


Mutually exclusive signaling signatures define the hepatic and pancreatic progenitor cell lineage divergence.

Rodríguez-Seguel E, Mah N, Naumann H, Pongrac IM, Cerdá-Esteban N, Fontaine JF, Wang Y, Chen W, Andrade-Navarro MA, Spagnoli FM.

Genes Dev. 2013 Sep 1;27(17):1932-46. doi: 10.1101/gad.220244.113.


CELDA -- an ontology for the comprehensive representation of cells in complex systems.

Seltmann S, Stachelscheid H, Damaschun A, Jansen L, Lekschas F, Fontaine JF, Nguyen-Dobinsky TN, Leser U, Kurtz A.

BMC Bioinformatics. 2013 Jul 17;14:228. doi: 10.1186/1471-2105-14-228.


Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts.

Neves M, Damaschun A, Mah N, Lekschas F, Seltmann S, Stachelscheid H, Fontaine JF, Kurtz A, Leser U.

Database (Oxford). 2013 Apr 18;2013:bat020. doi: 10.1093/database/bat020. Print 2013.


DNA microarray and miRNA analyses reinforce the classification of follicular thyroid tumors.

Jacques C, Guillotin D, Fontaine JF, Franc B, Mirebeau-Prunier D, Fleury A, Malthiery Y, Savagner F.

J Clin Endocrinol Metab. 2013 May;98(5):E981-9. doi: 10.1210/jc.2012-4006. Epub 2013 Apr 8.


Using cited references to improve the retrieval of related biomedical documents.

Ortuño FM, Rojas I, Andrade-Navarro MA, Fontaine JF.

BMC Bioinformatics. 2013 Mar 27;14:113. doi: 10.1186/1471-2105-14-113.


Estrogen-related receptor alpha modulates lactate dehydrogenase activity in thyroid tumors.

Mirebeau-Prunier D, Le Pennec S, Jacques C, Fontaine JF, Gueguen N, Boutet-Bouzamondo N, Donnart A, Malthièry Y, Savagner F.

PLoS One. 2013;8(3):e58683. doi: 10.1371/journal.pone.0058683. Epub 2013 Mar 13.


CXCL5 limits macrophage foam cell formation in atherosclerosis.

Rousselle A, Qadri F, Leukel L, Yilmaz R, Fontaine JF, Sihn G, Bader M, Ahluwalia A, Duchene J.

J Clin Invest. 2013 Mar;123(3):1343-7. doi: 10.1172/JCI66580. Epub 2013 Feb 8.


Adding protein context to the human protein-protein interaction network to reveal meaningful interactions.

Schaefer MH, Lopes TJ, Mah N, Shoemaker JE, Matsuoka Y, Fontaine JF, Louis-Jeune C, Eisfeld AJ, Neumann G, Perez-Iratxeta C, Kawaoka Y, Kitano H, Andrade-Navarro MA.

PLoS Comput Biol. 2013;9(1):e1002860. doi: 10.1371/journal.pcbi.1002860. Epub 2013 Jan 3.


Development and application of a DNA microarray-based yeast two-hybrid system.

Suter B, Fontaine JF, Yildirimman R, Raskó T, Schaefer MH, Rasche A, Porras P, Vázquez-Álvarez BM, Russ J, Rau K, Foulle R, Zenkner M, Saar K, Herwig R, Andrade-Navarro MA, Wanker EE.

Nucleic Acids Res. 2013 Feb 1;41(3):1496-507. doi: 10.1093/nar/gks1329. Epub 2012 Dec 28.


HIPPIE: Integrating protein interaction networks with experiment based quality scores.

Schaefer MH, Fontaine JF, Vinayagam A, Porras P, Wanker EE, Andrade-Navarro MA.

PLoS One. 2012;7(2):e31826. doi: 10.1371/journal.pone.0031826. Epub 2012 Feb 14.


The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text.

Krallinger M, Vazquez M, Leitner F, Salgado D, Chatr-Aryamontri A, Winter A, Perfetto L, Briganti L, Licata L, Iannuccelli M, Castagnoli L, Cesareni G, Tyers M, Schneider G, Rinaldi F, Leaman R, Gonzalez G, Matos S, Kim S, Wilbur WJ, Rocha L, Shatkay H, Tendulkar AV, Agarwal S, Liu F, Wang X, Rak R, Noto K, Elkan C, Lu Z, Dogan RI, Fontaine JF, Andrade-Navarro MA, Valencia A.

BMC Bioinformatics. 2011 Oct 3;12 Suppl 8:S3. doi: 10.1186/1471-2105-12-S8-S3.


PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries.

Barbosa-Silva A, Fontaine JF, Donnard ER, Stussi F, Ortega JM, Andrade-Navarro MA.

BMC Bioinformatics. 2011 Nov 9;12:435. doi: 10.1186/1471-2105-12-435.

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